WASHINGTON – The Trump administration separated thousands more migrant children from their parents at the U.S. border than previously has been made public, according to an investigative report released Thursday, but the federal tracking system has been so poor that the precise number is hazy.

According to the report issued by the inspector general for the Department of Health and Human Services, the separated children include 118 taken between July and early November – after the administration halted a short-lived family separation policy that provoked a political firestorm and public outrage.

The report estimates that thousands of additional youngsters were taken into government custody from early in the Trump administration, months before the government announced it would separate parents and children in order to criminally prosecute their parents, through late last spring.

Previous administrations also separated minors from adults at the border in some instances, usually when they suspected the child was smuggled, or the parent appeared to be unfit. The latest report documents a sharp increase in separations under President Donald Trump.

Based on available records, separated children accounted for 0.3 percent of all unaccompanied minors taken into HHS custody in late 2016, near the end of the Obama administration. By August 2017, the percentage had increased more than tenfold, to 3.6 percent.

A large number of the separated children were released from federal custody before a court order last June that required federal officials to track carefully the status of some 2,500 separated children and submit regular updates on their status to a federal judge.

Immigration enforcement officials say their biggest reason for transferring youngsters into HHS custody is that their parents had criminal histories. But information on the parents’ criminal records often was so sketchy, the report said, that it is unclear whether the separations were warranted or whether the children could be safely returned to their parents.

The findings draw fresh attention to the flawed data systems and poor communication between federal agencies, which left officials responsible for housing children and vetting their potential sponsors uncertain whether they had been split apart from relatives with whom they arrived.

Asked Wednesday morning whether those systems are now adequate, assistant HHS inspector general Ann Maxwell replied, “The jury is still out on that.”

The 24-page report is the first in a series of “issue briefs” the inspector general’s office is planning this year to shed light on the government’s system of care for unaccompanied migrant children, most of whom enter the country across the southern border. Trump has made stopping the flow of undocumented immigrants into the country a defining issue of his White House tenure, prompting the longest partial shutdown in U.S. history by demanding that Congress pay for a border wall.

The report also focuses on the housing of foreign minors already in the United States in a network of facilities run by contractors and scattered around the country. The shelters serve as way stations for the youngsters while the Office of Refugee Resettlement, part of HHS’s Administration for Children and Families, looks for potential sponsors to house and care for them as they await immigration hearings.

Last fall, the Department of Homeland Security produced an unpublished report documenting the chaos triggered by the family separations the resulted from Trump’s shortlived “zero tolerance” crackdown.

Among other things, the DHS report found that 860 migrant children were kept in Border Patrol holding cells longer than three days and that inadequate steps were taken to track the identities of children too young to talk.

The cohort of migrant children and teenagers in government custody without their parents reached an all-time high late last year, even though the number of unaccompanied minors detained after crossing the border – about 50,000 in fiscal 2018 – was less than during surges in 2014 and 2016.

But the youngsters tended to stay longer in the refugee office’s custody; by November, the average length of stay had risen to 90 days. Part of the reason for longer stays was a policy the administration adopted the middle of last year in which everyone living in the household of a person willing to sponsor a minor was required to give fingerprints to the FBI. The requirement prompted some potential sponsors to shy away, slowing the search for suitable placements.

The administration abandoned that requirement last month, saying it was not providing useful information. But it kept another policy in which federal health officials are allowed to share with immigration enforcement officials information about adults they are screening as possible guardians.

In June, HHS’s refugee office opened a giant tent city in Tornillo, Texas, to house the ballooning number of migrant children, and more than 6,000 passed through it. After repeated complaints, including over inadequate background checks for the staff, HHS officials said last week that they had moved out all the children and were closing it down.